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Single-cell and spatial multiomic inference of gene regulatory networks using SCRIPro.
- Source :
-
Bioinformatics . Jul2024, Vol. 40 Issue 7, p1-18. 18p. - Publication Year :
- 2024
-
Abstract
- Motivation The burgeoning generation of single-cell or spatial multiomic data allows for the characterization of gene regulation networks (GRNs) at an unprecedented resolution. However, the accurate reconstruction of GRNs from sparse and noisy single-cell or spatial multiomic data remains challenging. Results Here, we present SCRIPro, a comprehensive computational framework that robustly infers GRNs for both single-cell and spatial multiomics data. SCRIPro first improves sample coverage through a density clustering approach based on multiomic and spatial similarities. Additionally, SCRIPro scans transcriptional regulator (TR) importance by performing chromatin reconstruction and in silico deletion analyses using a comprehensive reference covering 1292 human and 994 mouse TRs. Finally, SCRIPro combines TR-target importance scores derived from multiomic data with TR-target expression levels to ensure precise GRN reconstruction. We benchmarked SCRIPro on various datasets, including single-cell multiomic data from human B-cell lymphoma, mouse hair follicle development, Stereo-seq of mouse embryos, and Spatial-ATAC-RNA from mouse brain. SCRIPro outperforms existing motif-based methods and accurately reconstructs cell type-specific, stage-specific, and region-specific GRNs. Overall, SCRIPro emerges as a streamlined and fast method capable of reconstructing TR activities and GRNs for both single-cell and spatial multiomic data. Availability and implementation SCRIPro is available at https://github.com/wanglabtongji/SCRIPro. [ABSTRACT FROM AUTHOR]
- Subjects :
- *GENETIC regulation
*HAIR follicles
*MULTIOMICS
*CHROMATIN
*MICE
Subjects
Details
- Language :
- English
- ISSN :
- 13674803
- Volume :
- 40
- Issue :
- 7
- Database :
- Academic Search Index
- Journal :
- Bioinformatics
- Publication Type :
- Academic Journal
- Accession number :
- 178887819
- Full Text :
- https://doi.org/10.1093/bioinformatics/btae466